Updated 2023-02-24

Running Eigen on the Cluster

Overview

  • Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
  • This guide will cover how to run Eigen on the Cluster.
  • The example used in this guide comes from this link.

Summary

  • Load the eigen/3.4.0 module.
  • You can now include any of the headers found in Eigen with #include <Eigen/<Header>> in your C++ files.
  • Compile and run your C++ program normally.

Walkthrough: Run Eigen on the Cluster

  • This walkthrough will run a C++ script that makes Eigen print out its version.
  • The C++ script can be found here
  • SBATCH script can be found here
  • You can transfer the files to your account on the cluster to follow along. The file transfer guide may be helpful.

Part 1: The SBATCH Script

#!/bin/bash
#SBATCH -JeigenTest
#SBATCH -A [Account] 
#SBATCH -N1 --ntasks-per-node=2
#SBATCH --mem-per-cpu=2G
#SBATCH -t3
#SBATCH -qinferno
#SBATCH -oReport-%j.out

cd $SLURM_SUBMIT_DIR
module load eigen/3.4.0
g++ eigenTest.cc
./a.out
  • The #SBATCH directives are standard, requesting just 3 minutes of walltime and 1 node with 2 cores. More on #SBATCH directives can be found in the Using Slurm on Phoenix Guide
  • $SLURM_SUBMIT_DIR is simply a variable that represents the directory you submit the SBATCH script from.
  • Output Files will also show up in this dir as well
  • module load eigen/3.4.0 loads the 3.4.0 version of Eigen. To see what Eigen versions are available, run module spider eigen, and load the one you want. The other module are dependencies that must be loaded before Eigen is loaded.
  • g++ eigenTest.cc compiles the C++ program.
  • p./a.out runs the C++ program.

Part 2: Submit Job and Check Status

  • Be sure to change to the directory that contains the SBATCH Script
  • Submit as normal, with <sbatch scriptname.sbatch>. In this case sbatch eigen.sbatch
  • Check job status with squeue --job <jobID>, replacing with the jobid returned after running sbatch
  • You can delete the job with scancel <jobID> , replacing with the jobid returned after running sbatch

Part 3: Collecting Results

  • In the directory where you submitted the SBATCH script, you should see a Report-<jobID>.out file, which contains the results of the job, an eigenTest.cc file which contains the C++ code, and an a.out executable. Use cat Report-<jobID>.out or open the file in a text editor to take a look.
  • Report-.out should look like this:
---------------------------------------
Begin Slurm Prolog: Dec-01-2022 00:41:40
Job ID:    130804
User ID:   svangala3
Account:   phx-pace-staff
Job name:  eigenTest
Partition: cpu-small
QOS:       inferno
---------------------------------------
 Eigen version : 4 . 0
---------------------------------------
Begin Slurm Epilog: Dec-01-2022 00:42:01
Job ID:        130804
Array Job ID:  _4294967294
User ID:       svangala3
Account:       phx-pace-staff
Job name:      eigenTest
Resources:     cpu=2,mem=4G,node=1
Rsrc Used:     cput=00:00:42,vmem=13132K,walltime=00:00:21,mem=0,energy_used=0
Partition:     cpu-small
QOS:           inferno
Nodes:         atl1-1-02-004-15-1
---------------------------------------
  • After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
  • Congratulations! You successfully ran a C++ Program using Eigen on the cluster.